Using version Version 5.13 (5.13.201807230) on OS X El Capitan.
I happen to have two novels by different authors called “Exodus”. To read whichever one I didn’t read last, I must clear the cache.
I’m afraid many book titles are not unique; perhaps a path name, partial path name or filesystem id and inode should be used instead. All have drawbacks if books are moved around. (No, I don’t use the bookshelf to manage my books. I had an arrangement I liked before I started using BookReader, and can’t use it on my phone.)
Thanks for a good product!